2MGN | pdb_00002mgn

Solution structure of a G-quadruplex bound to the bisquinolinium compound Phen-DC3

• PDB DOI: https://doi.org/10.2210/pdb2MGN/pdb
• NAKB: 2MGN
• BMRB: 19594

• Classification: DNA
• Mutation(s): No 


• Deposited: 2013-11-01 Released: 2014-01-22 
• Deposition Author(s): Chung, W.J., Heddi, B., Hamon, F., Teulade-Fichou, M.P., Phan, A.T.

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Experimental Data Snapshot

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Literature

Solution Structure of a G-quadruplex Bound to the Bisquinolinium Compound Phen-DC3.

Chung, W.J., Heddi, B., Hamon, F., Teulade-Fichou, M.P., Phan, A.T.

(2014) Angew Chem Int Ed Engl 53: 999-1002

• PubMed: 24356977 
• DOI: https://doi.org/10.1002/anie.201308063
• Primary Citation Related Structures: 
  2MGN


• PubMed Abstract: 
  

  Phen-DC3 is a highly promising compound that specifically targets G-quadruplexes, with potent biological effects observed in vivo. We used NMR spectroscopy to solve the structure of the complex formed between Phen-DC3 and an intramolecular G-quadruplex derived from the c-myc promoter. Structural information revealed that Phen-DC3 interacts with the quadruplex through extensive π-stacking with guanine bases of the top G-tetrad. On the basis of our structure, modifications are proposed for the development of this compound for selective targeting of a specific G-quadruplex conformation.

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Organizational Affiliation: 
• School of Physical and Mathematical Sciences, Nanyang Technological University, Singapore 637371 (Singapore).

Biological Assembly 1  

Biological assembly 1 assigned by authors.

Macromolecule Content 

• Total Structure Weight: 8.24 kDa 
• Atom Count: 555 
• Modeled Residue Count: 24 
• Deposited Residue Count: 24 
• Unique nucleic acid chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Length	Organism	Image
5'-D(*TP*GP*AP*GP*GP*GP*TP*GP*GP*TP*GP*AP*GP*GP*GP*TP*GP*GP*GP*GP*AP*AP*GP*G)-3'	A	24	N/A

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PQ3	B [auth A]	N2,N9-bis(1-methylquinolin-3-yl)-1,10-phenanthroline-2,9-dicarboxamide C34 H26 N6 O2 CTOLNXAGCUTHBW-UHFFFAOYSA-P

Experimental Data & Validation

Experimental Data

• Method: SOLUTION NMR
• Conformers Calculated: 100 
• Conformers Submitted: 10 
• Selection Criteria: structures with the lowest energy 

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-01-22 
Deposition Author(s): Chung, W.J., Heddi, B., Hamon, F., Teulade-Fichou, M.P., Phan, A.T.

Revision History  

• Version 1.0: 2014-01-22
  Type: Initial release
  
• Version 1.1: 2014-02-05
  Changes: Database references
• Version 1.2: 2014-04-02
  Changes: Non-polymer description
• Version 1.3: 2023-06-14
  Changes: Data collection, Database references, Derived calculations, Other
• Version 2.0: 2024-05-15
  Changes: Data collection, Database references, Non-polymer description